[English] 日本語
Yorodumi
- EMDB-5427: Cryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5427
TitleCryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
Map dataReconstruction of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
Sample
  • Sample: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
  • Virus: Nudaurelia capensis omega virus
KeywordsTime-resolved / T=4 / quasi-equivalence / maturation
Biological speciesNudaurelia capensis omega virus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsMatsui T / Lander GC / Khayat R / Johnson JE
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Subunits fold at position-dependent rates during maturation of a eukaryotic RNA virus.
Authors: Tsutomu Matsui / Gabriel C Lander / Reza Khayat / John E Johnson /
Abstract: Effective antiviral agents are difficult to develop because of the close relationship between the cell biology of the virus and host. However, viral capsid maturation, the in vivo process where the ...Effective antiviral agents are difficult to develop because of the close relationship between the cell biology of the virus and host. However, viral capsid maturation, the in vivo process where the particle transitions from a noninfectious provirion to an infectious virion, is an ideal process to interrupt because the provirion is usually fragile and the conversion to the virion often involves large conformational changes and autocatalytic chemistry that can be hampered by small molecules. The Nudaurelia capensis omega virus (N omegaV) is one of the few eukaryotic viruses where this process can be investigated in vitro with a variety of biophysical methods, allowing fundamental chemical and structural principles of the maturation to be established. It has a T = 4 quasi-equivalent capsid with a dramatic maturation pathway that includes a particle size reduction of 100 A and an autocatalytic cleavage. Here we use cryo-EM and difference maps, computed at three time points following maturation initiation, to show that regions of N omegaV subunit folding are maturation dependent and occur at rates determined by their quasi-equivalent position in the capsid, explaining the unusual kinetics of the maturation cleavage. This study shows that folding is rapid and peptide chain self-cleavage occurs early for subunits adjacent to 3-fold and 5-fold icosahedral symmetry elements and that folding is slower in regions where molecular switches are required for the formation of the proper interfacial contacts. The results connect viral maturation to the well-studied assembly-dependent folding that occurs in the formation of cellular complexes.
History
DepositionMay 29, 2012-
Header (metadata) releaseJun 4, 2012-
Map releaseJun 4, 2012-
UpdateJun 4, 2012-
Current statusJun 4, 2012Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_5427.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
Voxel sizeX=Y=Z: 2.768 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.54007864 - 6.85695648
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 553.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.7682.7682.768
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z553.600553.600553.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-4.5406.8570.000

-
Supplemental data

-
Sample components

-
Entire : Nudaurelia capensis omega virus (NwV) capsid at 30min time point ...

EntireName: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
Components
  • Sample: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
  • Virus: Nudaurelia capensis omega virus

-
Supramolecule #1000: Nudaurelia capensis omega virus (NwV) capsid at 30min time point ...

SupramoleculeName: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation
type: sample / ID: 1000 / Oligomeric state: Icosahedral virus / Number unique components: 1

-
Supramolecule #1: Nudaurelia capensis omega virus

SupramoleculeName: Nudaurelia capensis omega virus / type: virus / ID: 1 / Name.synonym: NwV (N omega V) / NCBI-ID: 12541 / Sci species name: Nudaurelia capensis omega virus / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: NwV (N omega V)
Host (natural)Organism: Lepidoptera (butterflies and moths) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 400 Å / T number (triangulation number): 4

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 5 / Details: 100mM NaOAc, 250mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 7sec before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateFeb 13, 2008
Image recordingNumber real images: 497 / Average electron dose: 16.5 e/Å2
Details: Data were collected using the Leginon automated electron microscopy package and data processing was performed using the Appion pipeline.
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: Data processing was performed using the Appion pipeline.
Number images used: 17174

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more